A totally automated on-line hydrolysis and analysis of proteins and peptides is being perfected through a CRADA, which is based on our recently developed method of acid hydrolysis ("Hydrolysis of Proteins and Peptides in a Hermetically-sealed Microcapillary Tube, J. Anal. Biochem. 1989"). The method would allow a complete analysis of proteins and peptides with greater accuracy especially for those amino acids that are acid labile. The manual version of this procedure has been successfully applied for the analysis of both research and regulatory samples including, various species of interferons, pertussis toxin and toxoids, hepatitis C vaccine, numerous AIDS-related peptides, erythropoietins. For the pertussis toxoid, special analytical conditions and were developed for 3-nitrotyrosine, a key modified amino acid as a result of toxoidation by tetranitromethane. For the erythropoietins, chromatographic methods were developed for the separation of oligosaccharides generated by enzymatic digestion of the glycoproteins and the complete carbohydrate composition was determined. For hepatitis C vaccine, the discrepancy between the results obtained by Lowry protein analysis and that determined by amino acid composition was resolved in favor of the latter.